I have been looking for the lyrics to Johnny's Gone Aloft and it turns out that it was Tom who went aloft not John. My brother thought he had seen the song in a book called Captain Whall's Sea Chanties and was possibly called Tom Bowline. Thank you Mudcat, for the link to the incredible Bodleian Library, I found it under the title of Tom Bowling! Now if someone knows the tune, we'll make it rise again, as a Christmas present to my mother, as this was one of the songs in her father's repetoire.

Tom Bowling
by Charles Dibdin

Here a sheer hulk lies poor Tom Bowling
The darling of our crew
No more he'll hear the tempest howling
For death has brought him to.
His form was the manliest beauty
His heart was kind and soft
Faithful below he did his duty
And now he's gone aloft.

Tom never from his word departed
His virtues were so rare
His friends were many and true-hearted
His poll was kind and fair
And then he'd sing so blythe and jolly
Ah! many's the time and oft
But mirth is turned to melancholy
For Tom is gone aloft.

Yet shall poor Tom find pleasant weather
When He, who all commands
Shall give to call life's crew together
The word to pipe all hands,
Thus death, who kings and tars dispatches
In vain Tom's life has doff'd
For tho' his body's under hatches
His soul has gone aloft.